Group information not updated when reactions are renamed

[pranasag]

Hi Brett et al,

I would like to submit an issue regarding the use of Groups/Subsystems. Two cases when it goes wrong:

• When renaming reactions with rxn.changeId(), the following happens: the group information is not updated, it seems, and the exported model does not any group/subsystems assigned to it. Also, slightly unrelated, but it seems that the reaction bound objects also do not get updated.

The next one seems to be duplicate, see #22

• When deleting reactions model.deleteReactionAndBounds(): the member is not removed from the group(s) it belonged to. COBRApy complains about loading such a SBML file, so now I have written a brute-force loop to check whether there are "ghost" members in each group.

Fixes would be appreciated!
Cheers
Pranas